//      dna_processing.h
//      
//      Copyright 2012 tqlong <tqlong@espada>
//      
//      This program is free software; you can redistribute it and/or modify
//      it under the terms of the GNU General Public License as published by
//      the Free Software Foundation; either version 2 of the License, or
//      (at your option) any later version.
//      
//      This program is distributed in the hope that it will be useful,
//      but WITHOUT ANY WARRANTY; without even the implied warranty of
//      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//      GNU General Public License for more details.
//      
//      You should have received a copy of the GNU General Public License
//      along with this program; if not, write to the Free Software
//      Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
//      MA 02110-1301, USA.

#ifndef DNA_PROCESSING_H
#define DNA_PROCESSING_H

#include <vector>
#include <string>
#include <ostream>

/** A list of sequences that has been extracted from the genome 
  * This is the main data class for gene algorithms
  */
class Sequences : public std::vector<std::string>
{
  typedef std::vector<std::string> __BASE;
 public:
  int n, n_gc;

  int max_length() const;
  void fasta_read(const std::string& fastaFile);
  std::ostream& print (std::ostream&o, bool isFile = false) const;
  void split(std::ostream&o, int length);
 public:
  std::vector<std::string> annotation_;
};


#endif
